Collapse weak clades below a confidence threshold.

Given a fully binary phylogeny with per-node confidence scores stored in tree$node.label, this helper collapses every internal node whose confidence falls below conf, effectively pruning low-support clades while retaining higher-confidence structure.

Usage

trim_tree(tree, conf, collapse_trivial = TRUE)

Arguments

tree

A binary phylo object whose node.label vector stores posterior/confidence values for internal nodes.

conf

Numeric threshold in $0,1$. Internal nodes with confidence below this value are collapsed.

collapse_trivial

Logical; if TRUE, collapses the trivial root-adjacent singleton split (1 tip vs the rest) into a root polytomy.

Value

A renumbered phylo object with low-confidence nodes collapsed.